Secondary structure and small RNA-seq evidence for dme-mir-2281

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:10222106-10222238 - TCCAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGAGCAGTACACGTA---TTATCTGCAG------CTGCAGATGCAAATGTATATGTATCTGTATCTG------TATCT--GCAGTAT-TGC-----AGTA-------TCGCTGCTTTATTCATATCCATG-------AGACGCGTCGCG
droSim1 chr3R:11233896-11234028 + GCCAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGAGCAGTACTCGTA---TTATCTGCAG------CTGCAGATGCAAATGTATATGTATCTGTATCTG------TATCT--GCAGTAT-TGC-----AGTA-------TCGCTGCTTTATTCGTATCCATG-------TGACGCGTCGCG
droSec1 super_0:11818438-11818570 + GCCAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGAGCAGTACTCGTA---TTATCTGCAG------CTGCAGATGCAAATGTATATGTATCTGTATCTG------TATCT--GCAGTAT-TGC-----AGTA-------TCGTTGCTTTATTCGTATCCATG-------TGACGCGTCGCG
droYak2 chr3R:16218838-16218961 + TCCAGTG-------------------------------------------------------------------------CATCCTACGGATGCCGAGCTGC------G---TTATCTGCAG------CTGCAGATGCAAATGTATCTGTATCTT--TCAG------TAT-T--GCAATGT-TGC-----AGTA-------TCTTTGCTTTATTCGTATCCGTG-------TGACGCGTCGCG
droEre2 scaffold_4770:9756449-9756546 - TCCAGTG-------------------------------------------------------------------------CATCCTACGGATGCCGAGCAT----C--G---TTATCTGCAG------CTGCAGATGCAAATGTA------------TCTG------TATCT--GCAGTAC-GGC-----------------------------TGTATCCGTG-------TGACGCGGCGCG
droAna3 scaffold_13117:2846333-2846460 - GTA----------------------------------------------------------------------------------------TCTCGAGATGCATCTGTAAGAGTATCTGCAT------CTGCAAATGTATCTGTATCTGTATCTGTATCTG------TATCT--GTATCTG-TGC-----AAGACTTGCCACCTCTCCTTTTCTCCTTTTCCTG-------AGCAAATGTCGC
dp4 chrXR_group8:8158458-8158593 + GCTAGTG-------------------------------------------------------------------------CCCACTACTGCCTTTGGCATGTATCTGTATCTGTACCCGTATCCGTATCCGTATCCGTTACTGTATCTGTATCTGTATCTG------TAGCT--GCTCTGAATGC-----AGTA-------TATA---TTTCATCAAATTTTTG-------TA----CTCGCA
droPer1 super_0:4124990-4125137 + GTAGGGGATCAGGCATGGCCAGGGGCAGCGGCAACGGCAGGGGCAGGGGCAGGGGCAGCTTTTCCAGGCT-------GTGCATCCTACGGATGGCAGGCTGTAC----------------------------------AACCGTATCGGCAGCCGTATCGG------TATCG--G---------------------------------------TGTATCTGTG-------TGACGCGTCGCG
droWil1 scaffold_181089:10073219-10073346 + CCTGGTAGAGAACGT-----------------------TGGGG--GAGGGGGGGGTTAGTTTTCCAGGCTCGCTGCAAAACATCCTACGATGTGAAAATTGT------G---A---------------------------AGG------------CTACTGAAA--GCG-GT--GCAATGC-GAG-----------------------------GAGAGCGACG-------CAATGCGACGCG
droVir3 scaffold_12928:2113057-2113188 + GTATCTATATCTGTA----------------------------------------------------------------------TATG------TATCTGT------ATCTGTATCTGTATCTGTATCTGTATCTGTATCTGTATCTGTATCTGTATCTG------TATCT--GTAT------C-----TATAT------TTGCTT----CTTTAAATCCGCCTCTTTCGAGACATTTATCC
droMoj3 scaffold_6654:2537235-2537365 + TTCAGTGAATCTGTATCTGTATCTGTATCTGTATCTG----------------------------------------------------------------------------TATCTGTAT------CTGTATCTGTATCTGTATCTGTATCTGTATCTGTATCTGTATCG--TATCTGT-ATC-----------------TGTATCTGTATCTGTATCTG----------TATTTGTATCT
droGri2 scaffold_14830:2155779-2155908 - GCGA-TG-------------------------------------------------------------------------TATCT--CGTATCTCGGCGAGTACGTCGC---------GCAT------CCGTATCTGCAAATGTATCTCTATCTATAGCTG------TATCTGAGCAATGTATGTAGTATAGTA-------TCTGTTGTT--GGGGTTTTCATA-------TTGCTTGTGCTG

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:10222106-10222238 - TCCAGTGCATCCTACGGATGTCGAGCAGTACACGTATTATCTGCAGCTGCAGATGCAAATGTATATGTATCTGTATCTGTATCTGCAGTATTGCAGTATCGCTGCTTTATTCATATCCATGAGACGCGTCGCG
droSim1 chr3R:11233896-11234028 + GCCAGTGCATCCTACGGATGTCGAGCAGTACTCGTATTATCTGCAGCTGCAGATGCAAATGTATATGTATCTGTATCTGTATCTGCAGTATTGCAGTATCGCTGCTTTATTCGTATCCATGTGACGCGTCGCG
droSec1 super_0:11818438-11818570 + GCCAGTGCATCCTACGGATGTCGAGCAGTACTCGTATTATCTGCAGCTGCAGATGCAAATGTATATGTATCTGTATCTGTATCTGCAGTATTGCAGTATCGTTGCTTTATTCGTATCCATGTGACGCGTCGCG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
GCCAGTGCATCCTACGGATGTCGAGC------AGTACTCGTAT---TATCTGCAGCTGCAGATGCAAATGTATATGTATCTGTATCTGTATCTGCA-GTATTGCAGTATCGCTGCTTTATTCGTATCCATGTGACGCGTCGCGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GCTAGTGCCCACTACTGCCTTTGGCATGTATCTGTATCTGTACCCGTATCCGTATCCGTATCCGTTACTGTATCTGTATCTGTATCTGTAGCTGCTCTGAATGCAGTATATA---TTTCATCAAATTTTTGTAC----TCGCASizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
.......................................................................ATCTGTATCTGTATCTGT......................................................1811.00101
.......................................................................ATCTGTATCTGTATCTGTA.....................................................1911.00101
......................................................................TATCTGTATCTGTATCTGTA.....................................................2011.00101

Secondary Structure

dm3

dG=-26.8,  p-value=0.009901

droSim1

dG=-26.8,  p-value=0.009901 dG=-25.9,  p-value=0.009901

droSec1

dG=-26.8,  p-value=0.009901 dG=-25.9,  p-value=0.009901

droYak2

dG=-19.6,  p-value=0.009901 dG=-18.7,  p-value=0.009901 dG=-18.6,  p-value=0.009901

droEre2

dG=-24.5,  p-value=0.009901

droAna3

dG=-7.6,  p-value=0.009901 dG=-7.6,  p-value=0.009901 dG=-7.5,  p-value=0.009901 dG=-7.5,  p-value=0.009901 dG=-7.5,  p-value=0.009901

dp4

dG=-10.8,  p-value=0.009901 dG=-10.6,  p-value=0.009901 dG=-10.5,  p-value=0.009901 dG=-10.5,  p-value=0.009901 dG=-10.2,  p-value=0.009901 dG=-8.4,  p-value=0.009901

droPer1

dG=-7.7,  p-value=0.009901 dG=-7.0,  p-value=0.009901 dG=-6.8,  p-value=0.009901 dG=-6.7,  p-value=0.009901

droWil1

dG=-4.7,  p-value=0.009901

droVir3

dG=-2.8,  p-value=0.009901 dG=-2.8,  p-value=0.009901 dG=-2.7,  p-value=0.009901 dG=-2.3,  p-value=0.009901 dG=-2.3,  p-value=0.009901

droMoj3

dG=-1.9,  p-value=0.009901 dG=-1.9,  p-value=0.009901 dG=-1.8,  p-value=0.009901 dG=-1.5,  p-value=0.009901 dG=-1.5,  p-value=0.009901

droGri2

dG=-7.6,  p-value=0.009901 dG=-7.6,  p-value=0.009901 dG=-7.3,  p-value=0.009901 dG=-7.2,  p-value=0.009901 dG=-7.2,  p-value=0.009901

Generated: 03/07/2013 at 04:54 PM